Biocompatible nanoparticles (NPs) of hydrophobic poly(benzyl malate) (PMLABe) were prepared by nanoprecipitation. The influence of nanoprecipitation parameters (initial PMLABe, addition rate, organic solvent/water ratio and stirring speed) were studied to optimize the resulting formulations in terms of hydrodynamic diameter (Dh) and dispersity (PDI). PMLABe NPs with a Dh of 160 nm and a PDI of 0.11 were isolated using the optimized nanoprecipitation conditions. A hydrophobic near infra-red (NIR) photothermally active nickel-bis(dithiolene) complex (Ni8C12) was then encapsulated into PMLABe NPs using the optimized nanoprecipitation conditions. The size and encapsulation efficiency of the NPs were measured, revealing that up to 50 weight percent (wt%) of Ni8C12 complex can efficiently be encapsulated with a slight increase in Dh of the corresponding Ni8C12-loaded NPs. Moreover, we have shown that NP encapsulating Ni8C12 were stable under storage conditions (4 °C) for at least 10 days. Finally, the photothermal properties of Ni8C12-loaded NPs were evaluated and a high photothermal efficiency (62.7 ± 6.0%) waswas measured with NPs incorporating 10 wt% of the Ni8C12 complex.